I'm about to upgrade our BDC/secondary DNS server. Are there any implications this may have or is it ok to just shut it down and rebuilt it? My first thought is it should be ok, but just wanted to make sure.

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I typically bring the new server up first, transfer any roles, add the necessary services, features and whatever else, give it time to replicate then shut down the services like DNS and DHCP on the old server for a little time to make sure everything is working properly. If it is, I uninstall each service leading up to demoting the domain controller.